Gene loci information

Transcript annotation

  • This transcript has been annotated as General transcription factor IIE subunit 1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g12007 g12007.t4 TTS g12007.t4 20303498 20303498
chr_1 g12007 g12007.t4 isoform g12007.t4 20303798 20304766
chr_1 g12007 g12007.t4 exon g12007.t4.exon1 20303798 20304766
chr_1 g12007 g12007.t4 cds g12007.t4.CDS1 20303799 20304734
chr_1 g12007 g12007.t4 TSS g12007.t4 20305027 20305027

Sequences

>g12007.t4 Gene=g12007 Length=969
ATATAGCTGAACTTCTTAAATTTGAGAAAAAGATGCTACGAGCCAGATTAACGCTTTTAA
AAAACGATAAATTTATGCAAGCAAGATTAAAAATGGAAACTGGAGTAGACGGAAAAGCAC
ATAAAGTGAATTATTACTTTATCAATTATAAAACTTTCGTTAATGTTATTAAATATAAAT
TGGATTTAATGAGAAAGAGACTTGAAACAGAGGAAAGAGACGCAACTGCTCGAGCTAATT
TTAAATGCACAAATTGCTCAAAACCTTTTACTGATCTTGAAGTTGATCAATTATTTGACC
TTAATACTGGTGAATTAAGATGTACCTATTGTGGGAGTTTAGTAGAAGAAGATATGGCAG
CAATGCCGCGAACAGATTCTCGATTAATGCTCGCAAAATTCAATGAGCAATTAGAACCAC
TTTATGATCTTTTAAAGCAAGCCGAAGGTATAAAATTGGCTCCTGAAGTTTTGGAACCAC
AGCCAATTGATATCGATGTAATTCGTGGAATAACTAAGCCATCTGAAATGATGCATAATG
AAGTGTGGTCAGGTGAAGCAACAAGATCAACATCAGGTTTCATGAATGAAGAGGCAAAGG
TTAATGTGACAATTGGAGAGATTGATACAGTTGATCAAAGTGCTCAAAAGAAAGAACGAC
CTGTTTGGATGACTGAAAGTACTGTGGTTTCTAAAGATGCTGAACAGGATGCTGAGTCAA
TGCTTGAAAAAGTAGCTCAAAGTGCAGTACAAGCAAGTTCATGGCAAACACCAGCACCAG
CTATCACAACCACATCTAAAAATAAGAAAGAAACTGAAGAAAATATCATGTCTGTTCTTT
TAGCACATGAAAAACAAACGACTAAAGCTAATAATGATGCCGTAAGGAACCTCAATAATC
AAGACGATTCCAGTGGTGGTGGTGACTCGAGCGGAGATGATGATGATGAAATCGATCGAA
CTGAAATTC

>g12007.t4 Gene=g12007 Length=312
MLRARLTLLKNDKFMQARLKMETGVDGKAHKVNYYFINYKTFVNVIKYKLDLMRKRLETE
ERDATARANFKCTNCSKPFTDLEVDQLFDLNTGELRCTYCGSLVEEDMAAMPRTDSRLML
AKFNEQLEPLYDLLKQAEGIKLAPEVLEPQPIDIDVIRGITKPSEMMHNEVWSGEATRST
SGFMNEEAKVNVTIGEIDTVDQSAQKKERPVWMTESTVVSKDAEQDAESMLEKVAQSAVQ
ASSWQTPAPAITTTSKNKKETEENIMSVLLAHEKQTTKANNDAVRNLNNQDDSSGGGDSS
GDDDDEIDRTEI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g12007.t4 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 56 117 1.1E-25
6 g12007.t4 MobiDBLite mobidb-lite consensus disorder prediction 240 260 -
7 g12007.t4 MobiDBLite mobidb-lite consensus disorder prediction 240 255 -
8 g12007.t4 MobiDBLite mobidb-lite consensus disorder prediction 274 312 -
10 g12007.t4 MobiDBLite mobidb-lite consensus disorder prediction 274 296 -
9 g12007.t4 MobiDBLite mobidb-lite consensus disorder prediction 297 312 -
3 g12007.t4 PANTHER PTHR13097 TRANSCRIPTION INITIATION FACTOR IIE, ALPHA SUBUNIT 1 296 7.0E-53
1 g12007.t4 Pfam PF02002 TFIIE alpha subunit 2 64 2.1E-8
2 g12007.t4 Pfam PF08271 TFIIB zinc-binding 70 107 1.7E-7
12 g12007.t4 ProSiteProfiles PS51344 TFE/IIEalpha-type HTH domain profile. 1 47 11.193
5 g12007.t4 SMART SM00531 tfiie3 1 118 1.7E-26
4 g12007.t4 SUPERFAMILY SSF57783 Zinc beta-ribbon 56 116 1.45E-19

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006367 transcription initiation from RNA polymerase II promoter BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values